Gaussian
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Also search this wiki for 'g09' for a couple of more examples.
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GaussView aka gview
ssh -X sunetid@corn # connect to corn with x11 forwarding module load gaussian # load the gaussian module gview # start up gview
You should see a graphical screen with a molecule on it. You can load gaussian .com files via File->Open
If you get some error about "display", likely your X11 forwarding isn't configured correctly.
There is another program called "gview" also installed on the system, so if you get the "graphical vi" text editor window, that's not the Gaussian gview. You probably forgot to load the module.
As of 2016-08-15 the GView errors out with an xcb errof with XQuartz v2.7.9 but it works fine with XQuartz 2.7.8
Gaussian
To start gaussian: 'module load gaussian', 'which g09'.
interactive example
bishopj@corn21:~$ module load gaussian bishopj@corn21:~$ g09 az.com bishopj@corn21:~$ cat az.com %chk=az #P RB3LYP 6-31G(D) FOPT FREQ=ReadIsotopes Azulene 0 1 C 0.0 0.0 2.7 C 0.0 0.0 -2.5 C 0.0 -1.2 1.9 C 0.0 1.2 1.9 C 0.0 -0.7 0.5 C 0.0 0.7 0.5 C 0.0 -1.6 -0.5 C 0.0 1.6 -0.5 C 0.0 -1.3 -1.9 C 0.0 1.3 -1.9 H 0.0 0.0 3.8 H 0.0 0.0 -3.6 H 0.0 -2.2 2.2 H 0.0 2.2 2.2 H 0.0 -2.7 -0.3 H 0.0 2.7 -0.3 H 0.0 -2.1 -2.6 H 0.0 2.1 -2.6 300 1.0 0.9804 12 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 bishopj@corn21:~$ ls -tlr az* -rw------- 1 bishopj root 415 Oct 26 2006 az.com -rw------- 1 bishopj operator 359570 Apr 15 20:06 az.log -rw------- 1 bishopj operator 2985984 Apr 15 20:06 az.chk bishopj@corn21:~$
job submission example
How to setup and run Gaussian (g09) calculation on Barley. Gaussian calculations must run on a single node.
Setup Gaussian Input (g09_example.com). Below is for O2. Make sure to specfiy %mem and %nproc. Here 4 processors and 8GB RAM (2GB/proc). %nproc must be equal or less then total number of processors on a single node (See Main Page#Technical_details). As of April 2012 max processors is 24.
%mem=8GB %nproc=4 %chk=g09_example.chk #t sp b3lyp/6-31g This is an example gaussian job file 0 3 O 0.00000 0.0000 0.0000 O 1.22000 0.0000 0.0000
Setup Job Script: g09_example.script
Important parameter "#$ -pe shm 4" requests a single node with 4 processors. Change number to change number of requested processors. Match value in %nproc.
Line "#$ -N example" sets $JOB_NAME to be g09_example so only need to change name of gaussian input name in a single place.
#!/bin/bash #$ -N g09_example #$ -cwd #$ -pe shm 4 module load gaussian #set the Gaussian scratch directory to the job-specifc temp dir export GAUSS_SCRDIR=$TMPDIR g09 $JOB_NAME.com $JOB_NAME.log
Submit the script:
qsub g09_example.script